Contacts of the strand formed by residues 335 - 342 (chain H) in PDB entry 3MLQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 335 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334H GLN* 1.3 85.6 - - - +
336H LEU* 1.3 64.6 + - - +
337H GLY* 3.6 36.0 - - - -
338H LEU* 4.6 11.6 + - + +
351H LEU* 4.2 19.1 - - + -
353H LEU* 3.4 20.4 - - + -
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Residues in contact with LEU 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C GLN* 5.1 7.6 - - - +
334H GLN* 4.4 17.7 - - + +
335H TYR* 1.3 83.4 - - - +
337H GLY* 1.3 59.8 + - - +
352H VAL* 2.9 38.0 + - + +
353H LEU 4.7 0.4 - - - -
354H ARG* 2.9 45.1 - - + +
360H LYS* 4.3 7.2 - - + -
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Residues in contact with GLY 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335H TYR* 3.6 27.6 - - - -
336H LEU* 1.3 81.2 - - - +
338H LEU* 1.3 62.1 + - - -
351H LEU* 3.6 3.3 - - - -
352H VAL* 2.7 37.5 + - - +
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Residues in contact with LEU 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335H TYR* 4.7 11.2 - - + +
337H GLY* 1.3 75.7 - - - -
339H GLU* 1.3 63.8 + - - +
349H ASP* 4.8 16.4 - - + +
350H TYR 3.2 20.9 - - - +
351H LEU* 4.4 9.6 - - + +
352H VAL* 4.7 0.4 - - - -
365H VAL* 5.0 11.7 - - + -
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Residues in contact with GLU 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338H LEU* 1.3 77.1 - - - +
340H THR* 1.3 70.6 + - - +
341H ARG* 2.7 35.7 + - - +
349H ASP* 3.9 3.1 - - - -
350H TYR* 3.0 35.6 + - - +
352H VAL* 4.0 15.3 - - + +
362H TYR* 3.5 13.9 + - + -
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Residues in contact with THR 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339H GLU* 1.3 80.6 - - - +
341H ARG* 1.3 77.8 + - - +
342H GLU* 6.1 1.3 - - + -
347H LYS* 5.4 7.0 - - + -
348H ARG 4.0 8.7 - - - +
349H ASP* 3.8 18.0 + - - +
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Residues in contact with ARG 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 5.2 4.6 - - - +
99D GLN* 3.5 23.9 + - - -
108D ILE* 5.8 4.9 - - + -
110D GLU* 4.4 7.7 + - - -
339H GLU* 2.7 35.2 + - - +
340H THR* 1.3 81.6 + - - +
342H GLU* 1.3 62.3 + - - +
343H VAL* 3.6 12.3 - - + +
346H VAL 3.1 1.6 - - - +
347H LYS* 3.2 4.9 - - - +
348H ARG 3.1 32.0 + - - -
350H TYR* 3.4 35.8 - - + -
362H TYR* 2.7 45.1 + - + -
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Residues in contact with GLU 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H THR* 6.1 2.0 - - + -
341H ARG* 1.3 75.0 - - - +
343H VAL* 1.3 68.4 + - - +
344H LEU 3.8 0.7 + - - -
346H VAL 3.1 6.3 - - - +
347H LYS* 4.1 21.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il